HHsearch alignment for GI: 254780406 and conserved domain: TIGR02988

>TIGR02988 YaaA_near_RecF S4 domain protein YaaA; InterPro: IPR014330 This small protein has a single S4 domain (IPR002942 from INTERPRO); it is also found in bacterial S4 ribosomal proteins, some pseudouridine synthases and tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members that are not near recF are found instead near dnaA and/or dnaN, the usual neighbours of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage..
Probab=96.92  E-value=0.0017  Score=41.76  Aligned_cols=55  Identities=22%  Similarity=0.312  Sum_probs=49.7

Q ss_pred             CCCCHHHHHHHHHCC-CCCHHHHHHHHHCCCEEECCEECCCCCEEECCCCEEEECC
Q ss_conf             677344788999886-8778999999986986999999240687807999799999
Q gi|254780406|r   10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG   64 (354)
Q Consensus        10 ~~~~~RL~K~la~~g-~~SRr~a~~lI~~G~V~Vng~~v~~~~~~v~~~d~v~vdg   64 (354)
T Consensus         5 ~tEyITLgQlLK~~~~i~sGG~AK~fL~e~~V~vNGe~e~RRGkKL~~gD~i~i~~   60 (60)
T TIGR02988         5 KTEYITLGQLLKELGIIDSGGQAKWFLQENEVLVNGELENRRGKKLYPGDVIEIPD   60 (60)
T ss_pred             CCCEECHHHHHHHHHHHCCHHHHHHHHHCCCEEECCEEECCCCCEECCCCEEEECC
T ss_conf             43416276786688562282578898706955547844045887004896688269